Aftermath: Manila
by avngstories
Summary: Clint Barton gets extracted from his worst mission ever.
1. Chapter 1

**A/N: Yeah, another cross over. Couldn't help myself. Timeline note: The **_**Bourne Legacy**_** events were going on at the same time as the **_**Bourne Supremacy **_**events, which was like 5 years before the **_**Avengers**_**. Oh, and I own nothing. Go buy something from Marvel and Ludlum.**

As the fishing boat continued its journey out to sea, he looked back over his shoulder at the woman. She was sitting on the floor of the deck, her eyes closed. Surely she was exhausted from the events of the past 12 hours. He looked back out to sea and held up the binoculars. This plan definitely fell into the Seemed Like A Good Idea At The Time category. He winced a little at the pain from the gunshot wound. He was pretty sure there were still bullet fragments in there somewhere. This mission had been tough from the beginning, but now his life had taken a turn for the surreal. The changes were permanent now. He still didn't know how to process it all. Natasha had been living with this curse for a good part of her life, and now he would be too. And then there were the rumors about Fury. _Fuck._ He sure as hell hoped he wasn't going to go bald. From the angle of the sun he could tell they less than an hour of daylight left. It would just be so much easier for the carrier to spot them in the light. He glanced over at the fisherman and his son. The man was showing the boy how to steer. Barton smiled a little. With a little luck, this tin can of a boat would survive.

He watched the water as 3 dolphins road the waves. They hadn't a care in the world. Damn, his body hurt. He was nearly done. As if reading his thoughts, he heard the doctor come up behind him. "How's the wound?" she asked quietly.

"Fine for now." He lied.

"Aaron, how long until we get to another place?" she asked wearily.

_With any luck, the fisherman will get us to the coordinates before dark, _he thought. "I'm not sure. Morning maybe."

"So did you mean it?" she asked.

"Mean what?"

"Did you mean that we could go anywhere?"

He sighed. _Damn_, he felt guilty for lying to her. But why the hell should he? This woman had lied to him for months, tortured him, and seemed able to justify it all to herself in the name of science. But he was Clint Barton, and guilt just seemed to come naturally.

"Eventually." Was all he could say.

Their conversation was interrupted by the boy yelling. Clint looked out and noticed the dolphins had disappeared. They boy's yells were soon joined by his father's. There words were a jumbled mess, but he heard the word he'd been hoping for. "American ship."

Marta started to look scared. "D-did they find us again?" she stammered out.

He continued to look out to sea. "It's going to be ok, Marta."

Thankfully, the commotion started before he had to say anything else. Out of nowhere, a Zodiac appeared. The captain continued his yelling, but he was drowned out by the sound of the sailor on the bullhorn.

"Stop where you are! Cut your engines now!"

The captain complied.

"Prepare to be boarded."

Marta screamed, but Barton held her by the shoulders. "You have to trust me Marta."

She nodded wordlessly. Three black clad figures appeared on the fishing boat. Marta raised her hands instinctively, but noticed that Aaron only moved forward. She wondered if he intended to fight them. But how could he? He was too injured and exhausted.

"Stop where you are." Yelled the anonymous operative. One figure moved to the wheelhouse to secure the captain the boy. The other two moved in front of the Americans.

"Agent Clint Barton, SHIELD clearance Alpha Two Alpha. Get me the fuck out of here."

The first agent jumped back and pulled off his face mask, shocked. "Really?" was all the poor boy could sputter out.

"Yeah, really."

The agent grabbed his radio, "Base! I've got an agent requesting extraction. Repeat, Barton, Alpha Two Alpha requesting extraction."

"Well get him the hell off that sorry excuse for a boat." Yelled a deep voice over the line.

The second masked figure moved forward and removed her mask. "Sir," she called back. "He's not alone."

The female agent looked to Barton for instruction. He stepped aside and finally turned to look at a gasping Marta Schering. "Take her into custody." Barton sighed.

"Yes sir!" she obeyed and moved forward to take Marta by the arm.

"Wait." He said. "No cuffs. She gave me aid."

The female agent pursed her lips, but complied. "Come with me." She ordered.

Barton could see the tears in Marta's eyes. She had finally realized that the day held a few more unpleasant surprises.

By this time more agents had boarded, and were moving toward Barton, first aid kits out. He sat down, and surrendered to their attention. Through half closed eyes, he could see the sun setting.


	2. Chapter 2

The first thing he could hear was the sound of the heart rate monitor beeping. Then his eyes managed to unstick themselves and he could see the ceiling. Surgery. Right. Bullet fragments. "Don't move yet, Agent Barton." Came a pleasant sounding voice. Must be a nurse. He heard mumbling outside the room. Then the sound of footsteps. Then the rather frightening face of Nick Fury looking down onto his own. "Welcome back, Barton." He said.

All Clint could do was moan. Anesthesia always sucked, but this time he felt like a bus was sitting on his head.

"Don't move too much, son. They had to give you about a quart of something to keep you down on the operating table." Fury grabbed a chair and sat down. He looked at Barton with a touch of sadness. "They probably overcompensated a bit. It might take them a while before they figure out the right dosages of medications for you."

Barton moaned again. "Please tell me you're real, sir."

Fury chuckled. "Real as you're ever gonna meet, Barton. Good work, son. And bringing in the doctor was good idea. She'll be of use."

"Is it over sir?"

"Yes, Barton it's over. Coulson just called in. Romanoff got Byer."

"Where? Where did she get him?" he mumbled back.

Nick Fury raised his head. "Between the eyes, I believe."

Clint Barton smiled as he faded back to sleep.


	3. Chapter 3

**A/N, All my stories stick to the same basic head cannon. These shorter crossovers add clues to the longer stories. This story is set about 2 years before **_**Benji's Dream**_** and 5 years before **_**Virginia.**_** I love playing with all these characters, but alas, they belong to Marvel and Universal- and ultimately Disney. Yes, I know Disney doesn't own Universal, but it's only a matter of time…**

So, back to poor Dr. Marta who just found out what it's like to have the whole truth withheld from you. (Not that SHE ever did anything like that, of course)

Marta sat on the narrow bed in the infirmary staring through the window in the door. She could see two guards on either side of it. A nurse had brought her clean clothes, food, and medication to ease the pain of her aching head and muscles. Other than that - nothing. They would tell her nothing about where she was or where Aaron was –wait -that wasn't even his name. Well, of course it wasn't his name. But his name wasn't Kenneth either. She'd heard him say Clint Barton. Was that it? Was that his real name? Did he even have a real name anymore? And was he ok? He should have been in surgery by now. Did they have a surgeon here? Wherever HERE was? It felt like a ship – a very large navy ship, but she couldn't be sure. It had been two hours and the hard gurney was starting to look comfortable enough to sleep on. As if reading her mind, the nurse returned with a pot of tea and a blanket. "Try to rest, ma'am." Was all the woman said before she left again. Marta sipped the tea and pulled the blanket over her lap. She leaned back and fell asleep within a few minutes. And since she succumbed to fatigue, she didn't see the tall man dressed in black looking at her through the window.

Marta woke up with a start. Every part of her body hurt from the hellacious ordeal of the last week. She wondered if they might offer her more pain killers. She slowly walked over to the window and knocked. The guard motioned her to stand back and he opened the door. "Is anyone ever going to talk to me?" she asked.

The man looked sympathetic. "I'll let them know you're awake. "

"H-how long was I out?" she asked.

"About 6 hours. We can have some more food brought in if you like."

She nodded. "Thank you."

He closed the door and she heard it lock. _So, they take good care of their prisoners here_, she mused.

A few minutes later, a dark figure covered the window. She heard the door open and a very tall man wearing a black eye patch walked into the room carrying a tray of food. He set it on the side table and sat himself down in the one chair in the room. It was pretty clear he was NOT medical personnel.

"Dr. Schering, how are you feeling?" he asked in a deep, haunting voice.

She felt her lip quiver. Damn it. "F-fine, I guess. Who are you?"

"That's not important right now, Dr."

"What are you doing to do to me?" she whispered.

"Do TO you, Dr.? Nothing. It's what I can do FOR you that you might want to know."

"What's that?"

"Protection, Dr. I can offer you protection from the people who are still after you."

She wrapped her arms tightly around her knees and started to shake. "Still?"

The scary man gave her a soft smile. "They won't give up. I'm sorry about that. They think you know too much."

She looked at the floor and stayed silent.

Nick Fury stood up and took a deep breath. "One question." He said.

She glanced at him, "What?"

"Answer one question for me: honestly and to the best of your ability, and I can assure you that you will stay safe." He moved closer to her so that she had no choice to look at his face, an incredibly scary one. She flinched, so he moved back and sat do down.

His voice was softer this time. "Dr. Schering, where did you get the formula?"

She startled and looked back over at him. "What? What do you mean?"

Fury sighed again. "I said 'honestly', Dr."

She shook her head. "I don't know what you're talking about."

"We analyzed the chems you gave Agent Barton. So, I'm going to ask again. Where did you get the formula?" He didn't sound as soft this time.

"L-lots of people worked on it. I don't know where it all came from."

Fury stood up in anger. "Fine you can stay in here until you decide you wanna talk. And if you don't, I'd be happy to drop you off back in Manila." He snorted and walked back out the door, slamming it behind him.

Marta felt tears welling up in her eyes and hugged her knees harder. She started rocking back and forth, sobbing. _How? How could he have known?_


	4. Chapter 4

Fury walked over to Barton's room and knocked. "Barton, you awake?"

"Yessir." Clint mumbled. He was now.

Fury walked in and sat down. "Can you walk yet?"

Barton nodded. "Where am I walking to?"

"I just saw that doctor. She's not cooperating." He sighed. "Coulson and Romanoff will be here in 2 hours. Do you think you can convince her to talk before they get here? It would be a whole lot easier for her that way."

"I can try, but I don't think she'll trust me anymore." Said Barton, attempting to get out of the bed without his gown falling open in front of Fury.

"Tell her that I said my offer is real. She tells the truth, she can stay."

Clint nodded again. "Can I get some clothes first, sir?"

As it turned out, walking wasn't the best idea, so a nurse sat him in a wheelchair. At least he had on sweatpants and a t-shirt now. The guards knocked on the door of the room that they were holding Dr. Schering in.

They opened the door and the nurse pushed Clint in. He looked a Marta sitting in the chair, appearing cleaned up and stronger, but very pissed. "Hey. You alright?" he asked.

She just looked at the floor. Barton folded his hands on his lap and waited. She gave in first. "Did you get that wound taken care of?"

He nodded. "Almost good as new." He smiled. "Marta, let me explain."

"No. I don't want to hear it." she spat

"Look. We don't have a whole lot time for this Marta. We need to talk. And you need talk."

"So that's why you're here? That goon sent you in to interrogate me?"

"We're not the bad guys."

"Well then who the hell are you?"

"That's kind of a long story. And I can't tell you all of it right now. But what I can tell you is that SHEILD is a security organization that monitors and protects against threats."

"SHEILD? Is that a real name or made up?"

"Yeah, I know, it's a stupid name. Anyway, Director Fury was telling the truth. Byer's people won't stop looking for you. And I can't protect you anymore. So, please, Marta, tell Fury what he wants to know?"

"That's his name? Fury?" she shook her head. "I still don't understand what he thinks it is I know."

"Yes you do."

She popped her head up to look at him. "How do I know he'll believe me?"

"He'll know the truth when he hears it, Marta."

She looked down again. "He won't."

"Just try. Try to give us chance?"

"What's happens to me if he doesn't?"

Barton shook his head. "Then he'll turn to over to the CIA. And they have as much reason to want you silent as Byer did."

"Did? What do you mean did?"

Clint pursed his lips. "Byer is dead."

Marta closed her eyes and looked up. "What's that mean for Outcome?"

"Outcome is dead too. And I think you deserve to stay off that list, Marta."

"Do you?"

"Yes, I do."

"Ok, I'll try. I'll tell that man what I know."

"Good." Barton smiled. "Guards!" he yelled.

They opened the door in a hurry. "Ask the Director to come in, please?"

"Right away, sir."

Clint clumsily rolled his wheelchair closer to Marta. "You're with friends here. I promise." He whispered. Marta wiped a tear from her eye.

Fury walked in a minute later. He leaned against a wall and folded his arms. "Where did you get the formula Dr. Schering?"

"I found it." she whispered.

"Found it? Found it where?" snapped Fury.

Barton raised his eyebrows. _Uh, oh._

"Can I start from the beginning?" she asked meekly.

"That's usually a good place, yes." Said Fury.

"When I was a graduate student at Oxford, my mother died. I went back to London to take care of her things. My mother's family was German. They came to England during the war. I didn't know a lot about them." She faltered at the thought of her mother.

"It's ok, go on." Said Clint.

Fury was silent.

"There was trunk full of papers and journals. I read through them and realized they must have belonged to her mother. They were scientific notes that must have belonged to my grandfather. They were separated by the war. She got out to London, but he didn't. He got caught in Germany."

Marta started shaking. "You're not going to believe me." She whispered again.

"Try me, doctor?" replied Fury.

"I didn't even know that kind of research was going in during the 30's. His work was amazing. His understanding of cellular biology was way ahead of his time."

Barton rolled forward again, not wanting to miss what she was saying in halting breaths.

She continued, "There was a journal. He kept a journal of his research and in that journal was theory of how to alter the mitochondrial functions of a cell."

She stopped talking and bent over, hugging her knees.

"Marta." Whispered Barton. "Keep going."

"I-I used that as a starting point for my doctoral research. And he was right! He was right! I don't know how, but my grandfather was right!" she rushed out.

"What was your grandfather's name, Dr.?" asked Fury in the freakn' lowest scariest voice Clint had ever heard.

Marta looked at Fury. "Abraham Erskine." She whispered.

Fury let out a sigh and almost a smile. "Good girl." He said.

End of Chapter 4

**A/N: Sorry this update took so long. The story can end here, or I can keep it going. Let me know what you think in a review.**

**I've been working hard on some original fiction. Check me out on under VAStories on FictionPress. I REALLY NEED BETA'S THERE!**


	5. Chapter 5

A/N: BIG thank you to all of you who have fav/followed this Aftermath: Manila. This story got the best response, so I'll start with it. All of the comments/reviews seemed to favor Marta, which I find interesting. Marta knowingly experimented on human beings to further her own research. Yes, she had a change of heart when she met Aaron, but I'm not sure I'm ready to let the good doctor off the hook so fast. Not to fear Marta fans, she's got an ace up her sleeve.

Aaaaand here we go…

She looked up at him, shocked at his response. "You believe me?"

Fury took a deep breath and walked closer to her. "I believe you, doctor."

She had no idea why, but he seemed to be sincere. "Ok, what else do you want from me?"

Fury was already back at the door. "Guards! Call the quarter master and ask her to find a bed for a new guest."

The, he turned to Aaron – no, no- Barton, and grabbed his wheelchair. "Come on Barton; get back to your room."

"Sir, can I talk to Dr. Schering alone?"

"Later. You and I need to have a chat first." The glance Fury shot her made Marta squirm a bit. It was a _'this is your fault'_ kind of look.

Fury and Barton left, but the door opened again a few seconds later. "Dr. Shering?" said the guard. "Please come with me and we'll get you settled in a room."

She followed silently behind. Once out in the hall, she tried not to stare at the modern looking interior of the aircraft carrier. These SHIELD people weren't like any military group she had ever seen. They were like something out of a sci/fi movie. After several twists and turns through the hallway, the guard pointed her to a small room.

"Someone will bring you fresh clothes and supplies shortly. Please stay here until they come for you. It's easy to get lost around here." He said and left.

How could this be happening? After being almost murdered, blow up, chased, almost murdered some more, and now kidnapped by scary Navy type people, Marta didn't know what was real anymore. That Fury man accepted her story without question. It was almost like he was expecting to hear it. Did he know? Had he heard about her grandfather's research? And what now? Clearly, she wasn't being held as prisoner, but what was next? Her old life was gone- her job, her reputation, her house. Most of the people she used to see every day were dead. It was all gone.

#

Clint settled back into the bed and lay still as the nurse adjusted his lines.

"I want you to stay in this bed until you're released. Got it Barton?"

"Yes sir." He waited for the nurse to leave. "What did you want to talk to me about sir?"

Fury pulled up a chair and sat down next to him. "Son, there's something you need to know about what they gave you."

_Oh shit!_ "What's that sir?"

"There could be side-effects."

"Um, sir?" Clint hesitated. "How do you know that?"

Fury gave him a wry smile. "Agent Barton, do you know how old I am?"

"No sir." There were only the rumors.

Fury leaned in and looked him in the eye. "I'm ninety years old."

Clint's mind stuck shut a minute, the statement setting in. Fury looked to be about sixty- a healthy, strong sixty. No amount of good living or surgery could make a ninety year old man look sixty. Clint scratched his face, indicating that he was indeed, still alive and waiting for Fury to continue.

"In early 1942, I was a stupid ambitious young man anxious to prove I belonged in the white man's Army. Somehow I found myself stationed in New York. I was sweeping a floor when a general approached me. I was scared shitless, wondering what it was I'd done wrong. All he said was, 'what would you do to become an officer?' Not sure what to say, I just told him whatever it took, sir. He snapped his fingers at me to follow him and that's what I did."

Fury stopped and stood up, pacing the room. "That was the day my life changed forever, Barton."

Clint nodded, not sure what to say, wondering what the hell happened next. Fury looked like he was about to talk again when his phone rang. "Yes? Good. Meet me in briefing room."

He looked at Clint again. "Sorry, Barton. Coulson and Romanoff are here. We'll talk later, but you keep everything I've said to yourself, understand."

"Of course sir."

"Good. Rest Agent Barton. This shit ain't over yet."

And ninety year old Nick Fury left the room.

#

p.s. you can find me and my new novel on twitter juliennelloyd


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